Altered alignment strategy based on whether trimming is skipped or not (b7f23787) · Commits · Chaos / Cutandrun

conf/modules.config

+1 −1

Original line number	Diff line number	Diff line
		@@ -170,7 +170,7 @@ if(params.run_trim_galore_fastqc && !params.skip_trimming) {
		if(params.run_alignment) {
		process {
		withName: '.*:ALIGN_BOWTIE2:BOWTIE2_ALIGN' {
		ext.args = '--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700'
		ext.args = { params.skip_trimming ? '--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700' : '--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700' }
		publishDir = [
		[
		path: { "${params.outdir}/02_alignment/${params.aligner}/target/log" },